tbuckley/cabot-search huggingface dataset:
Crocetin Regulates Functions of Neural Stem Cells to Generate New Neurons for Cerebral Ischemia Recovery
Authors: Zhongqing Liu, Zhaojun Wang, Zhanchi Zhu, Jing Hong, Leisha Cui, Ying Hao, Guosheng Cheng, Rui Tan
Journal: Advanced Healthcare Materials (2023)

Many neurons undergo apoptosis after ischemic stroke. In the brain, neurogenesis has the potential for neuronal replacement and can be activated by external conditions to repair the injury. Crocetin (CRO), naturally extracted from the plant saffron, acts as a neuroprotective agent for ischemic stroke. However, the underlying mechanism remains unknown. In this work, the effect of CRO on neural stem cell (NSC) behaviors and subventricular zone neurogenesis is investigated. Initially, NSCs are incubated with different concentrations of CRO to detect the cell proliferation and differentiation in vitro. Second, ischemic stroke induced rats are treated with CRO using nimodipine (NMDP) as a comparison. The behavioral functions, infarcted volume, and apoptotic Nissl bodies of rats are noticeably improved after CRO-treatment, comparable to those of NMDP. In addition, the increased regional cerebral blood flow and promoted neuronal differentiation are achieved by CRO-treatment. Brain tissue examination shows significantly increased neuronal regeneration in the focal ischemic injury area. Meanwhile, the length of neurites is prolonged, indicating that CRO could potentially promote neurite extension to enhance cell-cell communication. These findings demonstrate that CRO facilitated the neuronal differentiation of NSCs by activating subventricular zone neurogenesis in damaged cortex and striatum sites to repair ischemic stroke.
Persistent mTORC1 activation due to loss of liver tuberous sclerosis complex 1 promotes liver injury in alcoholic hepatitis
Authors: Xiaojuan Chao, Shaogui Wang, Xiaowen Ma, Chen Zhang, Hui Qian, Sha Neisha Williams, Zhaoli Sun, Zheyun Peng, Wanqing Liu, Feng Li, Namratha Sheshadri, Wei-Xing Zong, Hong-Min Ni, Wen-Xing Ding
Journal: Hepatology (2023)

Background and Aims: The aim of the study was to investigate the role and mechanisms of tuberous sclerosis complex 1 (TSC1) and mechanistic target of rapamycin complex 1 (mTORC1) in alcohol-associated liver disease. Approach and Results: Liver-specific Tsc1 knockout (L- Tsc1 KO) mice and their matched wild-type mice were subjected to Gao-binge alcohol. Human alcoholic hepatitis (AH) samples were also used for immunohistochemistry staining, western blot, and quantitative real-time PCR (q-PCR) analysis. Human AH and Gao-binge alcohol-fed mice had decreased hepatic TSC1 and increased mTORC1 activation. Gao-binge alcohol markedly increased liver/body weight ratio and serum alanine aminotransferase levels in L- Tsc1 KO mice compared with Gao-binge alcohol-fed wild-type mice. Results from immunohistochemistry staining, western blot, and q-PCR analysis revealed that human AH and Gao-binge alcohol-fed L- Tsc1 KO mouse livers had significantly increased hepatic progenitor cells, macrophages, and neutrophils but decreased HNF4α-positive cells. Gao-binge alcohol-fed L- Tsc1 KO mice also developed severe inflammation and liver fibrosis. Deleting Tsc1 in cholangiocytes but not in hepatocytes promoted cholangiocyte proliferation and aggravated alcohol-induced ductular reactions, fibrosis, inflammation, and liver injury. Pharmacological inhibition of mTORC1 partially reversed hepatomegaly, ductular reaction, fibrosis, inflammatory cell infiltration, and liver injury in alcohol-fed L- Tsc1 KO mice. Conclusions: Our findings indicate that persistent activation of mTORC1 due to the loss of cholangiocyte TSC1 promotes liver cell repopulation, ductular reaction, inflammation, fibrosis, and liver injury in Gao-binge alcohol-fed L- Tsc1 KO mice, which phenocopy the pathogenesis of human AH.
Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut
Authors: Jason P. Lynch, Coral González-Prieto, Analise Z. Reeves, Sena Bae, Urmila Powale, Neha P. Godbole, Jacqueline M. Tremblay, Florian I. Schmidt, Hidde L. Ploegh, Vikram Kansra, Jonathan N. Glickman, John M. Leong, Charles B. Shoemaker, Wendy S. Garrett, Cammie F. Lesser
Journal: Cell Host & Microbe (2023)
A vision transformer for decoding surgeon activity from surgical videos
Authors: Dani Kiyasseh, Runzhuo Ma, Taseen F. Haque, Brian J. Miles, Christian Wagner, Daniel A. Donoho, Animashree Anandkumar, Andrew J. Hung
Journal: Nature Biomedical Engineering (2023)

Abstract The intraoperative activity of a surgeon has substantial impact on postoperative outcomes. However, for most surgical procedures, the details of intraoperative surgical actions, which can vary widely, are not well understood. Here we report a machine learning system leveraging a vision transformer and supervised contrastive learning for the decoding of elements of intraoperative surgical activity from videos commonly collected during robotic surgeries. The system accurately identified surgical steps, actions performed by the surgeon, the quality of these actions and the relative contribution of individual video frames to the decoding of the actions. Through extensive testing on data from three different hospitals located in two different continents, we show that the system generalizes across videos, surgeons, hospitals and surgical procedures, and that it can provide information on surgical gestures and skills from unannotated videos. Decoding intraoperative activity via accurate machine learning systems could be used to provide surgeons with feedback on their operating skills, and may allow for the identification of optimal surgical behaviour and for the study of relationships between intraoperative factors and postoperative outcomes.
Baseline PET radiomics outperform the IPI risk score for prediction of outcome in diffuse large B-cell lymphoma
Authors: Jakoba Johanna Eertink, Gerben JC Zwezerijnen, Martijn Heymans, Simone Pieplenbosch, Sanne Elisabeth Wiegers, Ulrich Dührsen, Andreas Hüttmann, Lars Kurch, Christine Hanoun, Pieternella J. Lugtenburg, Sally Barrington, N. George Mikhaeel, Luca Ceriani, Emanuele Zucca, Sandor Czibor, Tamás Györke, Martine E.D. Chamuleau, Otto S Hoekstra, Henrica CW De Vet, Ronald Boellaard, Josée M. Zijlstra
Journal: Blood (2023)
Deep-learning-based semantic segmentation of autonomic nerves from laparoscopic images of colorectal surgery: an experimental pilot study
Authors: Shigehiro Kojima, Daichi Kitaguchi, Takahiro Igaki, Kei Nakajima, Yuto Ishikawa, Yuriko Harai, Atsushi Yamada, Younae Lee, Kazuyuki Hayashi, Norihito Kosugi, Hiro Hasegawa, Masaaki Ito
Journal: International Journal of Surgery (2023)

Background: The preservation of autonomic nerves is the most important factor in maintaining genitourinary function in colorectal surgery; however, these nerves are not clearly recognisable, and their identification is strongly affected by the surgical ability. Therefore, this study aimed to develop a deep learning model for the semantic segmentation of autonomic nerves during laparoscopic colorectal surgery and to experimentally verify the model through intraoperative use and pathological examination. Materials and methods: The annotation data set comprised videos of laparoscopic colorectal surgery. The images of the hypogastric nerve (HGN) and superior hypogastric plexus (SHP) were manually annotated under a surgeon’s supervision. The Dice coefficient was used to quantify the model performance after five-fold cross-validation. The model was used in actual surgeries to compare the recognition timing of the model with that of surgeons, and pathological examination was performed to confirm whether the samples labelled by the model from the colorectal branches of the HGN and SHP were nerves. Results: The data set comprised 12 978 video frames of the HGN from 245 videos and 5198 frames of the SHP from 44 videos. The mean (±SD) Dice coefficients of the HGN and SHP were 0.56 (±0.03) and 0.49 (±0.07), respectively. The proposed model was used in 12 surgeries, and it recognised the right HGN earlier than the surgeons did in 50.0% of the cases, the left HGN earlier in 41.7% of the cases and the SHP earlier in 50.0% of the cases. Pathological examination confirmed that all 11 samples were nerve tissue. Conclusion: An approach for the deep-learning-based semantic segmentation of autonomic nerves was developed and experimentally validated. This model may facilitate intraoperative recognition during laparoscopic colorectal surgery.
Nanotechnologies for Physiology-Informed Drug Delivery to the Lymphatic System
Authors: Katharina Maisel, Claire A. McClain, Amanda Bogseth, Susan N. Thomas
Journal: Annual Review of Biomedical Engineering (2023)

Accompanying the increasing translational impact of immunotherapeutic strategies to treat and prevent disease has been a broadening interest across both bioscience and bioengineering in the lymphatic system. Herein, the lymphatic system physiology, ranging from its tissue structures to immune functions and effects, is described. Design principles and engineering approaches to analyze and manipulate this tissue system in nanoparticle-based drug delivery applications are also elaborated.
Prognosis and conditional nomogram of cervical spine fracture in patients with severe spinal cord injury: a multicenter retrospective study
Authors: Jinfeng Huang, Kang Yan, Chenyu Wu, Quan-Chang Tan, Hao Bai, Jing Wang, Bo Liao, Zi-Xiang Wu
Journal: International Journal of Surgery (2023)

Cervical spine fractures with severe spinal cord injury (SCI) are common following cervical spine trauma and are associated with a high mortality rate. Understanding the mortality patterns of patients with cervical spine fractures and severe SCI can offer valuable evidence to surgeons and family members who are required to make critical healthcare decisions. The authors aimed to evaluate the instantaneous death risk and conditional survival (CS) of such patients and developed conditional nomograms to account for different periods of survivors and predict the survival rates.Their instantaneous death risks were calculated using the hazard function, and the Kaplan-Meier method was used to evaluate the survival rates. Cox regression was used to choose the variables for the construction of the nomograms. The area under the receiver operating characteristic curve and calibration plots were used to validate the performance of the nomograms.The authors finally included 450 patients with cervical spine fractures and severe SCI using propensity score matching. The instantaneous death risk was the highest during the first 12 months after injury. Surgical treatment can help decrease the instantaneous death risk quickly, especially in early-term surgery. The 5-year CS increased constantly from 73.3% at baseline to 88.0% after 2 years of survival. Conditional nomograms were constructed at baseline and in those who survived for 6 and 12 months. The area under the receiver operating characteristic curve and calibration curves indicated that the nomograms had a good performance.Their results improve our understanding of the instantaneous death risk of patients in different periods following injury. CS demonstrated the exact survival rate among medium-term and long-term survivors. Conditional nomograms are suitable for different survival periods in predicting the probability of survival. Conditional nomograms help in understanding the prognosis and improve the shared decision-making approaches.
Carbapenem-resistant Pseudomonas aeruginosa in intensive care units increase mortality as an emerging global threat
Authors: Muthupandian Saravanan, Melaku A. Belete, Jesu Arockiaraj
Journal: International Journal of Surgery (2023)

Saravanan, Muthupandian PhD; Belete, Melaku Ashagrie MSc; Arockiaraj, Jesu PhD Author Information
Reply to Li and Colleagues
Authors: Christian P Kratz, Dmitrii Smirnov, Robert Autry, Natalie Jäger, Sebastian M Waszak, Anika Großhennig, Riccardo Berutti, Mareike Wendorff, Pierre Hainaut, Stefan M Pfister, Holger Prokisch, Tim Ripperger, David Malkin
Journal: JNCI Journal of the National Cancer Institute (2023)
Early and late recurrence patterns of pancreatic ductal adenocarcinoma after pancreaticoduodenectomy: a multicenter study
Authors: Xiu-Ping Zhang, Shuai Xu, Yuan-Xing Gao, Zhi-Ming Zhao, Guo-Dong Zhao, Ming-Gen Hu, Xiang-Long Tan, Wan Yee Lau, Rong Liu
Journal: International Journal of Surgery (2023)

Background: Survival after pancreaticoduodenectomy (PD) for pancreatic ductal adenocarcinoma (PDAC) remains poor because of high incidences of recurrence. The risk factors, patterns, and long-term prognosis in patients with early recurrence and late recurrence (ER and LR) for PDAC after PD were studied. Methods: Data from patients who underwent PD for PDAC were analyzed. Recurrence was divided into ER (ER ≤1 years) and LR (LR &gt;1 years) using the time to recurrence after surgery. Characteristics and patterns of initial recurrence, and postrecurrence survival (PRS) were compared between patients with ER and LR. Results: Among the 634 patients, 281 (44.3%) and 249 (39.3%) patients developed ER and LR, respectively. In the multivariate analysis, preoperative CA19-9 levels, resection margin status, and tumor differentiation were significantly associated with both ER and LR, while lymph node metastasis and perineal invasion were associated with LR. Patients with ER, when compared with patients with LR, showed a significantly higher proportion of liver-only recurrence ( P &lt;0.05), and worse median PRS (5.2 vs. 9.3 months, P &lt;0.001). Lung-only recurrence had a significantly longer PRS when compared with liver-only recurrence ( P &lt;0.001). Multivariate analysis demonstrated that ER and irregular postoperative recurrence surveillance were independently associated with a worse prognosis ( P &lt;0.001). Conclusion: The risk factors for ER and LR after PD are different for PDAC patients. Patients who developed ER had worse PRS than those who developed LR. Patients with lung-only recurrence had a significantly better prognosis than those with other recurrent sites.
Clonal architecture evolution in Myeloproliferative Neoplasms: from a driver mutation to a complex heterogeneous mutational and phenotypic landscape
Authors: Nabih Maslah, Lina Benajiba, Stephane Giraudier, Jean-Jacques Kiladjian, Bruno Cassinat
Journal: Leukemia (2023)

Abstract Myeloproliferative neoplasms are characterized by the acquisition at the hematopoietic stem cell level of driver mutations targeting the JAK/STAT pathway. In addition, they also often exhibit additional mutations targeting various pathways such as intracellular signalling, epigenetics, mRNA splicing or transcription. The natural history of myeloproliferative neoplasms is usually marked by a chronic phase of variable duration depending on the disease subtype, which can be followed by an accelerated phase or transformation towards more aggressive diseases such as myelofibrosis or acute leukemia. Besides, recent studies revealed important new information about the rates and mechanisms of sequential acquisition and selection of mutations in hematopoietic cells of myeloproliferative neoplasms. Better understanding of these events has been made possible in large part with the help of novel techniques that are now available to precisely decipher at the single cell level both the clonal architecture and the mutation-induced cell modifications. In this review, we will summarize the most recent knowledge about the mechanisms leading to clonal selection, how clonal architecture complexity can explain disease heterogeneity, and the impact of clonal evolution on clinical evolution.
Increased blood flow of spinal cord lesion after decompression improves neurological recovery of degenerative cervical myelopathy: an intraoperative ultrasonography-based prospective cohort study
Authors: Guoliang Chen, Chengkai Lin, Zhengya Zhu, Kuileung Tong, Shiming Li, Hongkun Chen, Zuofeng Xu, Ningning Chen, Xizhe Liu, Shaoyu Liu
Journal: International Journal of Surgery (2023)

Surgical decompression is a highly effective therapy for degenerative cervical myelopathy (DCM), but the mechanisms of neurological recovery following decompression remain unclear. This study aimed to evaluate the spinal cord blood flow status after sufficient decompression by intraoperative contrast-enhanced ultrasonography (CEUS) and to analyze the correlation between neurological recovery and postdecompressive spinal cord blood perfusion in DCM.Patients with multilevel DCM were treated by ultrasound-guided modified French-door laminoplasty using a self-developed rongeur. Neurological function was evaluated using the modified Japanese Orthopaedic Association (mJOA) score preoperatively and at 12 months postoperatively. Spinal cord compression and cervical canal enlargement before and after surgery were assessed by magnetic resonance imaging and computerized tomography. The decompression status was evaluated in real time by intraoperative ultrasonography, while the spinal cord blood flow after sufficient decompression was assessed by CEUS. Patients were categorized as favourable (≥50%) or unfavourable (<50%) recovery according to the recovery rate of the mJOA score at 12 months postoperatively.Twenty-nine patients were included in the study. The mJOA scores were significantly improved in all patients from 11.2±2.1 preoperatively to 15.0±1.1 at 12 months postoperatively, with an average recovery rate of 64.9±16.2%. Computerized tomography and intraoperative ultrasonography confirmed adequate enlargement of the cervical canal and sufficient decompression of the spinal cord, respectively. CEUS revealed that patients with favourable neurological recovery had a greater increased blood flow signal in the compressive spinal cord segment after decompression.In DCM, intraoperative CEUS can clearly reflect spinal cord blood flow. Patients with increased blood perfusion of the spinal cord lesion immediately after surgical decompression tended to achieve greater neurological recovery.
MetAAA trial patients show superior quality of life compared to patients under regular surveillance for small AAA: a single-center retrospective cohort study
Authors: Johannes Klopf, Robin Willixhofer, Andreas Scheuba, Lukas Fuchs, Anna Sotir, Anders Wanhainen, Christine Brostjan, Christoph Neumayer, Wolf Eilenberg
Journal: International Journal of Surgery (2023)

Abdominal aortic aneurysm (AAA) is a multifactorial vascular disease associated with high morbidity and mortality. Currently, surgical intervention is the only treatment option, and there is no drug therapy available for AAA. Hence, surveillance of AAA until indication for surgery may impact patient quality of life (QoL). There is a paucity of high-quality observational data on health status and QoL, particularly among AAA patients participating in randomized controlled trials. The objective of this study was to compare the QoL scores of AAA patients on surveillance to those of AAA patients enrolled in the MetAAA trial.Overall, 54 MetAAA trial patients and 23 AAA patients under regular surveillance for small AAA (part of a longitudinal monitoring study) were asked to complete three established and validated (in total 561 longitudinally collected) QoL questionnaires: the 36-Item Short Form Health Survey (SF-36), the Aneurysm Symptom Rating Questionnaire (ASRQ), and the Aneurysm-Dependent Quality of Life questionnaire (ADQoL).A superior health status and QoL was found in AAA patients participating in the MetAAA trial compared to AAA patients under regular surveillance. In detail, MetAAA trial patients showed superior general health perception ( P =0.012), higher energy level ( P =0.036) as well as enhanced emotional well-being ( P =0.044) and fewer limitations due to general malaise ( P =0.021), which was subsequently reflected in an overall superior current QoL score ( P =0.039) compared to AAA patients under regular surveillance.AAA patients enrolled in the MetAAA trial showed superior health status and QoL compared to AAA patients under regular surveillance.
Top 10 research priorities for irritable bowel syndrome: results of a James Lind Alliance priority setting partnership
Authors: Christopher J Black, Yvonne A McKenzie, Morgan Scofield-Marlowe, Peter Setter, Maryrose Tarpey, Alexander C Ford, Helen West, Esther Southey, Julie Thompson, Christopher J Black, Maura Corsetti, Hazel A Everitt, Alexander C Ford, David Greenwood, Pauline Hunt, Lesley Kirkpatrick, Yvonne McKenzie, Rona Moss-Morris, Christine Pollard, Morgan Scofield-Marlowe, Peter Setter, Margaret Surginor, Kristina Staley
Journal: The Lancet. Gastroenterology & hepatology (2023)
Analgesic effects of combined transversus abdominis plane block and intramuscular electrical stimulation in patients undergoing cytoreductive surgery followed by hyperthermic intraperitoneal chemotherapy: a randomized controlled trial
Authors: Hyun-Chang Kim, Jinyoung Park, Jinyoung Oh, Minjae Kim, Eun Jung Park, Seung Hyuk Baik, Young Song
Journal: International Journal of Surgery (2023)

To evaluate the analgesic efficacy of a four-quadrant transversus abdominis plane (4QTAP) block and a combination of 4QTAP block with needle electrical twitch and intramuscular electrical stimulation (NETOIMS) in patients undergoing cytoreductive surgery (CRS) followed by hyperthermic intraperitoneal chemotherapy (HIPEC).Eighty-one patients who underwent CRS followed by HIPEC were included in this study. Patients were randomly assigned to one of three groups: group 1 (intravenous patient-controlled analgesia, control group), group 2 (preoperative 4QTAP block), and group 3 (preoperative 4QTAP block and postoperative NETOIMS). The primary study endpoint was the pain score assessed by the visual analog scale (VAS: 0, no pain; 10, worst imaginable pain) on postoperative day (POD) 1.The VAS pain score on POD 1 was significantly lower in group 2 than in group 1 (6.0±1.7 and 7.6±1.9, P =0.004), whereas that in group 3 was significantly lower than that in groups 1 and 2 ( P <0.001 and P =0.004, respectively). Opioid consumption and nausea and vomiting incidence during POD 7 were significantly lower in group 3 than in groups 1 and 2. Gait speed and peak cough flow on POD 4 and 7, as well as the quality of recovery (QoR)-40 score on POD 4, were significantly higher in group 3 than in groups 1 and 2.The combination of a 4QTAP block with NETOIMS provided more effective analgesia than a 4QTAP block alone after CRS, followed by HIPEC, and enhanced functional restoration and quality of recovery.
Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia
Authors: Zhenhua Li, Ti-Cheng Chang, Jacob J Junco, Meenakshi Devidas, Yizhen Li, Wenjian Yang, Xin Huang, Dale J Hedges, Zhongshan Cheng, Mary Shago, Andrew J. Carroll, Nyla A. Heerema, Julie M Gastier-Foster, Brent L. Wood, Michael J. Borowitz, Lauren Sanclemente, Elizabeth A. Raetz, Stephen P. Hunger, Eleanor Feingold, Tracie C. Rosser, Stephanie L. Sherman, Mignon L. Loh, Charles G. Mullighan, Jiyang Yu, Gang Wu, Philip J Lupo, Karen R Rabin, Jun J. Yang
Journal: Blood (2023)